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404.html
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<a class="navbar-brand me-2" href="https://amr-for-r.org/index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="https://amr-for-r.org/index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9081</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9082</small>
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CLAUDE.html
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<a class="navbar-brand me-2" href="index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9081</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9082</small>
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<a class="navbar-brand me-2" href="index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9081</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9082</small>
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articles/AMR.html
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9081</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9082</small>
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@@ -91,7 +91,7 @@
website update since they are based on randomly created values and the website update since they are based on randomly created values and the
page was written in <a href="https://rmarkdown.rstudio.com/" class="external-link">R page was written in <a href="https://rmarkdown.rstudio.com/" class="external-link">R
Markdown</a>. However, the methodology remains unchanged. This page was Markdown</a>. However, the methodology remains unchanged. This page was
generated on 27 June 2026.</p> generated on 03 July 2026.</p>
<div class="section level2"> <div class="section level2">
<h2 id="introduction">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a> <h2 id="introduction">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a>
</h2> </h2>
@@ -147,21 +147,21 @@ make the structure of your data generally look like this:</p>
</tr></thead> </tr></thead>
<tbody> <tbody>
<tr class="odd"> <tr class="odd">
<td align="center">2026-06-27</td> <td align="center">2026-07-03</td>
<td align="center">abcd</td> <td align="center">abcd</td>
<td align="center">Escherichia coli</td> <td align="center">Escherichia coli</td>
<td align="center">S</td> <td align="center">S</td>
<td align="center">S</td> <td align="center">S</td>
</tr> </tr>
<tr class="even"> <tr class="even">
<td align="center">2026-06-27</td> <td align="center">2026-07-03</td>
<td align="center">abcd</td> <td align="center">abcd</td>
<td align="center">Escherichia coli</td> <td align="center">Escherichia coli</td>
<td align="center">S</td> <td align="center">S</td>
<td align="center">R</td> <td align="center">R</td>
</tr> </tr>
<tr class="odd"> <tr class="odd">
<td align="center">2026-06-27</td> <td align="center">2026-07-03</td>
<td align="center">efgh</td> <td align="center">efgh</td>
<td align="center">Escherichia coli</td> <td align="center">Escherichia coli</td>
<td align="center">R</td> <td align="center">R</td>

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articles/AMR.md
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**Note:** values on this page will change with every website update **Note:** values on this page will change with every website update
since they are based on randomly created values and the page was written since they are based on randomly created values and the page was written
in [R Markdown](https://rmarkdown.rstudio.com/). However, the in [R Markdown](https://rmarkdown.rstudio.com/). However, the
methodology remains unchanged. This page was generated on 27 June 2026. methodology remains unchanged. This page was generated on 03 July 2026.
## Introduction ## Introduction
@@ -51,9 +51,9 @@ structure of your data generally look like this:
| date | patient_id | mo | AMX | CIP | | date | patient_id | mo | AMX | CIP |
|:----------:|:----------:|:----------------:|:---:|:---:| |:----------:|:----------:|:----------------:|:---:|:---:|
| 2026-06-27 | abcd | Escherichia coli | S | S | | 2026-07-03 | abcd | Escherichia coli | S | S |
| 2026-06-27 | abcd | Escherichia coli | S | R | | 2026-07-03 | abcd | Escherichia coli | S | R |
| 2026-06-27 | efgh | Escherichia coli | R | S | | 2026-07-03 | efgh | Escherichia coli | R | S |
### Needed R packages ### Needed R packages

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articles/AMR_for_Python.html
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9081</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9082</small>
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articles/AMR_with_tidymodels.html
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9081</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9082</small>
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articles/EUCAST.html
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9081</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9082</small>
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articles/PCA.html
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9081</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9082</small>
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articles/WHONET.html
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@@ -30,7 +30,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9081</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9082</small>
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articles/WISCA.html
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9081</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9082</small>
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articles/datasets.html
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9081</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9082</small>
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@@ -80,7 +80,7 @@
<main id="main" class="col-md-9"><div class="page-header"> <main id="main" class="col-md-9"><div class="page-header">
<img src="../logo.svg" class="logo" alt=""><h1>Download data sets for download / own use</h1> <img src="../logo.svg" class="logo" alt=""><h1>Download data sets for download / own use</h1>
<h4 data-toc-skip class="date">27 June 2026</h4> <h4 data-toc-skip class="date">03 July 2026</h4>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/main/vignettes/datasets.Rmd" class="external-link"><code>vignettes/datasets.Rmd</code></a></small> <small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/main/vignettes/datasets.Rmd" class="external-link"><code>vignettes/datasets.Rmd</code></a></small>
<div class="d-none name"><code>datasets.Rmd</code></div> <div class="d-none name"><code>datasets.Rmd</code></div>

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articles/index.html
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9081</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9082</small>
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authors.html
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<a class="navbar-brand me-2" href="index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9081</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9082</small>
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index.html
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@@ -33,7 +33,7 @@
<a class="navbar-brand me-2" href="index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9081</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9082</small>
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@@ -85,7 +85,7 @@
<ul> <ul>
<li>Provides an <strong>all-in-one solution</strong> for antimicrobial resistance (AMR) data analysis in a One Health approach</li> <li>Provides an <strong>all-in-one solution</strong> for antimicrobial resistance (AMR) data analysis in a One Health approach</li>
<li> <li>
<strong>Peer-reviewed</strong>, used in over 175 countries, available in 28 languages</li> <strong>Peer-reviewed</strong>, used in over 175 countries, cites over 100 times, available in 28 languages</li>
<li>Generates <strong>antibiograms</strong> - WISCA for empiric coverage estimates, or traditional/syndromic for AMR surveillance</li> <li>Generates <strong>antibiograms</strong> - WISCA for empiric coverage estimates, or traditional/syndromic for AMR surveillance</li>
<li>Provides the <strong>full microbiological taxonomy</strong> of ~97 000 distinct species and extensive info of ~620 antimicrobial drugs</li> <li>Provides the <strong>full microbiological taxonomy</strong> of ~97 000 distinct species and extensive info of ~620 antimicrobial drugs</li>
<li>Applies <strong>CLSI 2011-2026</strong> and <strong>EUCAST 2011-2026</strong> clinical and veterinary breakpoints, and ECOFFs, for MIC and disk zone interpretation</li> <li>Applies <strong>CLSI 2011-2026</strong> and <strong>EUCAST 2011-2026</strong> clinical and veterinary breakpoints, and ECOFFs, for MIC and disk zone interpretation</li>
@@ -120,6 +120,7 @@
<p><a href="./countries_large.png" target="_blank"><img src="./countries.png" align="right" style="max-width: 300px;"></a></p> <p><a href="./countries_large.png" target="_blank"><img src="./countries.png" align="right" style="max-width: 300px;"></a></p>
<p>Since its first public release in early 2018, this R package has been used in almost all countries in the world. Click the map to enlarge and to see the country names.</p> <p>Since its first public release in early 2018, this R package has been used in almost all countries in the world. Click the map to enlarge and to see the country names.</p>
<p>With the help of contributors from all corners of the world, the <code>AMR</code> package is available in <img src="lang_en.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> English, <img src="lang_ar.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> Arabic, <img src="lang_bn.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> Bengali, <img src="lang_zh.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> Chinese, <img src="lang_cs.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> Czech, <img src="lang_da.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> Danish, <img src="lang_nl.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> Dutch, <img src="lang_fi.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> Finnish, <img src="lang_fr.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> French, <img src="lang_de.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> German, <img src="lang_el.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> Greek, <img src="lang_hi.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> Hindi, <img src="lang_id.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> Indonesian, <img src="lang_it.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> Italian, <img src="lang_ja.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> Japanese, <img src="lang_ko.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> Korean, <img src="lang_no.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> Norwegian, <img src="lang_pl.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> Polish, <img src="lang_pt.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> Portuguese, <img src="lang_ro.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> Romanian, <img src="lang_ru.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> Russian, <img src="lang_es.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> Spanish, <img src="lang_sw.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> Swahili, <img src="lang_sv.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> Swedish, <img src="lang_tr.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> Turkish, <img src="lang_uk.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> Ukrainian, <img src="lang_ur.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> Urdu, and <img src="lang_vi.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> Vietnamese. Antimicrobial drug (group) names and colloquial microorganism names are provided in these languages.</p> <p>With the help of contributors from all corners of the world, the <code>AMR</code> package is available in <img src="lang_en.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> English, <img src="lang_ar.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> Arabic, <img src="lang_bn.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> Bengali, <img src="lang_zh.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> Chinese, <img src="lang_cs.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> Czech, <img src="lang_da.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> Danish, <img src="lang_nl.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> Dutch, <img src="lang_fi.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> Finnish, <img src="lang_fr.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> French, <img src="lang_de.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> German, <img src="lang_el.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> Greek, <img src="lang_hi.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> Hindi, <img src="lang_id.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> Indonesian, <img src="lang_it.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> Italian, <img src="lang_ja.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> Japanese, <img src="lang_ko.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> Korean, <img src="lang_no.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> Norwegian, <img src="lang_pl.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> Polish, <img src="lang_pt.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> Portuguese, <img src="lang_ro.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> Romanian, <img src="lang_ru.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> Russian, <img src="lang_es.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> Spanish, <img src="lang_sw.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> Swahili, <img src="lang_sv.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> Swedish, <img src="lang_tr.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> Turkish, <img src="lang_uk.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> Ukrainian, <img src="lang_ur.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> Urdu, and <img src="lang_vi.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> Vietnamese. Antimicrobial drug (group) names and colloquial microorganism names are provided in these languages.</p>
<p>The <code>AMR</code> package was cited <a href="https://scholar.google.com/citations?view_op=view_citation&amp;hl=en&amp;citation_for_view=sAoHvIgAAAAJ:0EnyYjriUFMC" class="external-link">over 100 times</a> in scientific research.</p>
</div> </div>
</div> </div>
<div class="section level2"> <div class="section level2">
@@ -191,9 +192,9 @@
<th align="left">Piperacillin/tazobactam + Tobramycin</th> <th align="left">Piperacillin/tazobactam + Tobramycin</th>
</tr></thead> </tr></thead>
<tbody><tr> <tbody><tr>
<td align="left">70% (64.7-75.2%)</td> <td align="left">69.9% (64.9-75.3%)</td>
<td align="left">93.6% (92.2-95.1%)</td> <td align="left">93.6% (92.1-95%)</td>
<td align="left">89.8% (87-92.5%)</td> <td align="left">89.9% (87-92.4%)</td>
</tr></tbody> </tr></tbody>
</table> </table>
<p>WISCA supports stratification by any clinical variable, so you can generate syndrome-specific or ward-specific coverage estimates:</p> <p>WISCA supports stratification by any clinical variable, so you can generate syndrome-specific or ward-specific coverage estimates:</p>
@@ -219,21 +220,21 @@
<tbody> <tbody>
<tr> <tr>
<td align="left">Clinical</td> <td align="left">Clinical</td>
<td align="left">74.6% (68.6-80.6%)</td> <td align="left">74.5% (68.6-80.5%)</td>
<td align="left">93.7% (92.1-95.1%)</td> <td align="left">93.7% (91.7-95.1%)</td>
<td align="left">90.4% (87-93.1%)</td> <td align="left">90.4% (87.1-93.1%)</td>
</tr> </tr>
<tr> <tr>
<td align="left">ICU</td> <td align="left">ICU</td>
<td align="left">57% (48.6-65.7%)</td> <td align="left">57% (48.6-65.6%)</td>
<td align="left">86.8% (83.6-89.8%)</td> <td align="left">86.7% (83.3-89.9%)</td>
<td align="left">82.9% (78.1-87.3%)</td> <td align="left">83% (78.1-87.5%)</td>
</tr> </tr>
<tr> <tr>
<td align="left">Outpatient</td> <td align="left">Outpatient</td>
<td align="left">56.9% (45.9-68.2%)</td> <td align="left">57.4% (46-69.1%)</td>
<td align="left">76.7% (70.6-82.3%)</td> <td align="left">76.7% (70.5-82.7%)</td>
<td align="left">68% (57.6-77.2%)</td> <td align="left">67.7% (57.3-77.4%)</td>
</tr> </tr>
</tbody> </tbody>
</table> </table>
@@ -391,11 +392,6 @@
<span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/summarise.html" class="external-link">summarise</a></span><span class="op">(</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/across.html" class="external-link">across</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="va">GEN</span>, <span class="va">TOB</span><span class="op">)</span>,</span> <span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/summarise.html" class="external-link">summarise</a></span><span class="op">(</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/across.html" class="external-link">across</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="va">GEN</span>, <span class="va">TOB</span><span class="op">)</span>,</span>
<span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>total_R <span class="op">=</span> <span class="va">resistance</span>,</span> <span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>total_R <span class="op">=</span> <span class="va">resistance</span>,</span>
<span> conf_int <span class="op">=</span> <span class="kw">function</span><span class="op">(</span><span class="va">x</span><span class="op">)</span> <span class="fu"><a href="reference/proportion.html">sir_confidence_interval</a></span><span class="op">(</span><span class="va">x</span>, collapse <span class="op">=</span> <span class="st">"-"</span><span class="op">)</span><span class="op">)</span><span class="op">)</span><span class="op">)</span></span> <span> conf_int <span class="op">=</span> <span class="kw">function</span><span class="op">(</span><span class="va">x</span><span class="op">)</span> <span class="fu"><a href="reference/proportion.html">sir_confidence_interval</a></span><span class="op">(</span><span class="va">x</span>, collapse <span class="op">=</span> <span class="st">"-"</span><span class="op">)</span><span class="op">)</span><span class="op">)</span><span class="op">)</span></span>
<span><span class="co">#&gt; ℹ `resistance()` assumes the EUCAST guideline and thus</span></span>
<span><span class="co">#&gt; considers the 'I' category susceptible. Set the `guideline`</span></span>
<span><span class="co">#&gt; argument or the `AMR_guideline` option to either "CLSI" or</span></span>
<span><span class="co">#&gt; "EUCAST", see `?AMR-options`.</span></span>
<span><span class="co">#&gt; ℹ This message will be shown once per session.</span></span>
<span><span class="co">#&gt; # A tibble: 3 × 5</span></span> <span><span class="co">#&gt; # A tibble: 3 × 5</span></span>
<span><span class="co">#&gt; ward GEN_total_R GEN_conf_int TOB_total_R TOB_conf_int</span></span> <span><span class="co">#&gt; ward GEN_total_R GEN_conf_int TOB_total_R TOB_conf_int</span></span>
<span><span class="co">#&gt; &lt;chr&gt; &lt;dbl&gt; &lt;chr&gt; &lt;dbl&gt; &lt;chr&gt; </span></span> <span><span class="co">#&gt; &lt;chr&gt; &lt;dbl&gt; &lt;chr&gt; &lt;dbl&gt; &lt;chr&gt; </span></span>

21
index.md
View File

@@ -2,8 +2,8 @@
- Provides an **all-in-one solution** for antimicrobial resistance (AMR) - Provides an **all-in-one solution** for antimicrobial resistance (AMR)
data analysis in a One Health approach data analysis in a One Health approach
- **Peer-reviewed**, used in over 175 countries, available in 28 - **Peer-reviewed**, used in over 175 countries, cites over 100 times,
languages available in 28 languages
- Generates **antibiograms** - WISCA for empiric coverage estimates, or - Generates **antibiograms** - WISCA for empiric coverage estimates, or
traditional/syndromic for AMR surveillance traditional/syndromic for AMR surveillance
- Provides the **full microbiological taxonomy** of ~97 000 distinct - Provides the **full microbiological taxonomy** of ~97 000 distinct
@@ -89,6 +89,10 @@ Swahili, ![](lang_sv.svg) Swedish, ![](lang_tr.svg) Turkish,
Vietnamese. Antimicrobial drug (group) names and colloquial Vietnamese. Antimicrobial drug (group) names and colloquial
microorganism names are provided in these languages. microorganism names are provided in these languages.
The `AMR` package was cited [over 100
times](https://scholar.google.com/citations?view_op=view_citation&hl=en&citation_for_view=sAoHvIgAAAAJ:0EnyYjriUFMC)
in scientific research.
## Practical examples ## Practical examples
### Filtering and selecting data ### Filtering and selecting data
@@ -183,7 +187,7 @@ wisca(example_isolates,
| Piperacillin/tazobactam | Piperacillin/tazobactam + Gentamicin | Piperacillin/tazobactam + Tobramycin | | Piperacillin/tazobactam | Piperacillin/tazobactam + Gentamicin | Piperacillin/tazobactam + Tobramycin |
|:---|:---|:---| |:---|:---|:---|
| 70% (64.7-75.2%) | 93.6% (92.2-95.1%) | 89.8% (87-92.5%) | | 69.9% (64.9-75.3%) | 93.6% (92.1-95%) | 89.9% (87-92.4%) |
WISCA supports stratification by any clinical variable, so you can WISCA supports stratification by any clinical variable, so you can
generate syndrome-specific or ward-specific coverage estimates: generate syndrome-specific or ward-specific coverage estimates:
@@ -199,9 +203,9 @@ wisca(example_isolates,
| Syndromic Group | Piperacillin/tazobactam | Piperacillin/tazobactam + Gentamicin | Piperacillin/tazobactam + Tobramycin | | Syndromic Group | Piperacillin/tazobactam | Piperacillin/tazobactam + Gentamicin | Piperacillin/tazobactam + Tobramycin |
|:---|:---|:---|:---| |:---|:---|:---|:---|
| Clinical | 74.6% (68.6-80.6%) | 93.7% (92.1-95.1%) | 90.4% (87-93.1%) | | Clinical | 74.5% (68.6-80.5%) | 93.7% (91.7-95.1%) | 90.4% (87.1-93.1%) |
| ICU | 57% (48.6-65.7%) | 86.8% (83.6-89.8%) | 82.9% (78.1-87.3%) | | ICU | 57% (48.6-65.6%) | 86.7% (83.3-89.9%) | 83% (78.1-87.5%) |
| Outpatient | 56.9% (45.9-68.2%) | 76.7% (70.6-82.3%) | 68% (57.6-77.2%) | | Outpatient | 57.4% (46-69.1%) | 76.7% (70.5-82.7%) | 67.7% (57.3-77.4%) |
**For AMR surveillance**, traditional antibiograms remain the right tool **For AMR surveillance**, traditional antibiograms remain the right tool
for tracking resistance per species over time: for tracking resistance per species over time:
@@ -310,11 +314,6 @@ example_isolates %>%
summarise(across(c(GEN, TOB), summarise(across(c(GEN, TOB),
list(total_R = resistance, list(total_R = resistance,
conf_int = function(x) sir_confidence_interval(x, collapse = "-")))) conf_int = function(x) sir_confidence_interval(x, collapse = "-"))))
#> ℹ `resistance()` assumes the EUCAST guideline and thus
#> considers the 'I' category susceptible. Set the `guideline`
#> argument or the `AMR_guideline` option to either "CLSI" or
#> "EUCAST", see `?AMR-options`.
#> ℹ This message will be shown once per session.
#> # A tibble: 3 × 5 #> # A tibble: 3 × 5
#> ward GEN_total_R GEN_conf_int TOB_total_R TOB_conf_int #> ward GEN_total_R GEN_conf_int TOB_total_R TOB_conf_int
#> <chr> <dbl> <chr> <dbl> <chr> #> <chr> <dbl> <chr> <dbl> <chr>

21
llms.txt
View File

@@ -2,8 +2,8 @@
- Provides an **all-in-one solution** for antimicrobial resistance (AMR) - Provides an **all-in-one solution** for antimicrobial resistance (AMR)
data analysis in a One Health approach data analysis in a One Health approach
- **Peer-reviewed**, used in over 175 countries, available in 28 - **Peer-reviewed**, used in over 175 countries, cites over 100 times,
languages available in 28 languages
- Generates **antibiograms** - WISCA for empiric coverage estimates, or - Generates **antibiograms** - WISCA for empiric coverage estimates, or
traditional/syndromic for AMR surveillance traditional/syndromic for AMR surveillance
- Provides the **full microbiological taxonomy** of ~97 000 distinct - Provides the **full microbiological taxonomy** of ~97 000 distinct
@@ -89,6 +89,10 @@ Swahili, ![](lang_sv.svg) Swedish, ![](lang_tr.svg) Turkish,
Vietnamese. Antimicrobial drug (group) names and colloquial Vietnamese. Antimicrobial drug (group) names and colloquial
microorganism names are provided in these languages. microorganism names are provided in these languages.
The `AMR` package was cited [over 100
times](https://scholar.google.com/citations?view_op=view_citation&hl=en&citation_for_view=sAoHvIgAAAAJ:0EnyYjriUFMC)
in scientific research.
## Practical examples ## Practical examples
### Filtering and selecting data ### Filtering and selecting data
@@ -183,7 +187,7 @@ wisca(example_isolates,
| Piperacillin/tazobactam | Piperacillin/tazobactam + Gentamicin | Piperacillin/tazobactam + Tobramycin | | Piperacillin/tazobactam | Piperacillin/tazobactam + Gentamicin | Piperacillin/tazobactam + Tobramycin |
|:---|:---|:---| |:---|:---|:---|
| 70% (64.7-75.2%) | 93.6% (92.2-95.1%) | 89.8% (87-92.5%) | | 69.9% (64.9-75.3%) | 93.6% (92.1-95%) | 89.9% (87-92.4%) |
WISCA supports stratification by any clinical variable, so you can WISCA supports stratification by any clinical variable, so you can
generate syndrome-specific or ward-specific coverage estimates: generate syndrome-specific or ward-specific coverage estimates:
@@ -199,9 +203,9 @@ wisca(example_isolates,
| Syndromic Group | Piperacillin/tazobactam | Piperacillin/tazobactam + Gentamicin | Piperacillin/tazobactam + Tobramycin | | Syndromic Group | Piperacillin/tazobactam | Piperacillin/tazobactam + Gentamicin | Piperacillin/tazobactam + Tobramycin |
|:---|:---|:---|:---| |:---|:---|:---|:---|
| Clinical | 74.6% (68.6-80.6%) | 93.7% (92.1-95.1%) | 90.4% (87-93.1%) | | Clinical | 74.5% (68.6-80.5%) | 93.7% (91.7-95.1%) | 90.4% (87.1-93.1%) |
| ICU | 57% (48.6-65.7%) | 86.8% (83.6-89.8%) | 82.9% (78.1-87.3%) | | ICU | 57% (48.6-65.6%) | 86.7% (83.3-89.9%) | 83% (78.1-87.5%) |
| Outpatient | 56.9% (45.9-68.2%) | 76.7% (70.6-82.3%) | 68% (57.6-77.2%) | | Outpatient | 57.4% (46-69.1%) | 76.7% (70.5-82.7%) | 67.7% (57.3-77.4%) |
**For AMR surveillance**, traditional antibiograms remain the right tool **For AMR surveillance**, traditional antibiograms remain the right tool
for tracking resistance per species over time: for tracking resistance per species over time:
@@ -310,11 +314,6 @@ example_isolates %>%
summarise(across(c(GEN, TOB), summarise(across(c(GEN, TOB),
list(total_R = resistance, list(total_R = resistance,
conf_int = function(x) sir_confidence_interval(x, collapse = "-")))) conf_int = function(x) sir_confidence_interval(x, collapse = "-"))))
#> ℹ `resistance()` assumes the EUCAST guideline and thus
#> considers the 'I' category susceptible. Set the `guideline`
#> argument or the `AMR_guideline` option to either "CLSI" or
#> "EUCAST", see `?AMR-options`.
#> ℹ This message will be shown once per session.
#> # A tibble: 3 × 5 #> # A tibble: 3 × 5
#> ward GEN_total_R GEN_conf_int TOB_total_R TOB_conf_int #> ward GEN_total_R GEN_conf_int TOB_total_R TOB_conf_int
#> <chr> <dbl> <chr> <dbl> <chr> #> <chr> <dbl> <chr> <dbl> <chr>

12
news/index.html
View File

@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9081</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9082</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -49,15 +49,15 @@
</div> </div>
<div class="section level2"> <div class="section level2">
<h2 class="pkg-version" data-toc-text="3.0.1.9081" id="amr-3019081">AMR 3.0.1.9081<a class="anchor" aria-label="anchor" href="#amr-3019081"></a></h2> <h2 class="pkg-version" data-toc-text="3.0.1.9082" id="amr-3019082">AMR 3.0.1.9082<a class="anchor" aria-label="anchor" href="#amr-3019082"></a></h2>
<p>Planned as v3.1.0, end of June 2026.</p> <p>Planned as v3.1.0, end of June 2026.</p>
<div class="section level4"> <div class="section level4">
<h4 id="breaking-changes-3-0-1-9081">Breaking Changes<a class="anchor" aria-label="anchor" href="#breaking-changes-3-0-1-9081"></a></h4> <h4 id="breaking-changes-3-0-1-9082">Breaking Changes<a class="anchor" aria-label="anchor" href="#breaking-changes-3-0-1-9082"></a></h4>
<ul><li>The former <em>kingdoms</em> Bacteria and Archaea are now each divided into four kingdoms with new top-level <em>domains</em> ‘Bacteria’ and ‘Archaea’ (Göker and Oren, 2024, DOI: 10.1099/ijsem.0.006242). Following this, a new <code>domain</code> column in the <code>microorganisms</code> data set was added, and more importantly, <code><a href="../reference/mo_property.html">mo_kingdom()</a></code> now returns the formal kingdom (e.g. <code>"Pseudomonadati"</code> instead of <code>"Bacteria"</code>). Use <code><a href="../reference/mo_property.html">mo_domain()</a></code> for the old behaviour. For non-prokaryotic kingdoms (Fungi, Protozoa, etc.), <code>kingdom</code> and <code>domain</code> are identical.</li> <ul><li>The former <em>kingdoms</em> Bacteria and Archaea are now each divided into four kingdoms with new top-level <em>domains</em> ‘Bacteria’ and ‘Archaea’ (Göker and Oren, 2024, DOI: 10.1099/ijsem.0.006242). Following this, a new <code>domain</code> column in the <code>microorganisms</code> data set was added, and more importantly, <code><a href="../reference/mo_property.html">mo_kingdom()</a></code> now returns the formal kingdom (e.g. <code>"Pseudomonadati"</code> instead of <code>"Bacteria"</code>). Use <code><a href="../reference/mo_property.html">mo_domain()</a></code> for the old behaviour. For non-prokaryotic kingdoms (Fungi, Protozoa, etc.), <code>kingdom</code> and <code>domain</code> are identical.</li>
<li>Faster parallel computing via the <code>future</code> package for <code><a href="../reference/as.sir.html">as.sir()</a></code> and <code><a href="../reference/antibiogram.html">wisca()</a></code>: a non-sequential plan (e.g. <code>future::plan(future::multisession)</code>) must be active before using <code>parallel = TRUE</code>.</li> <li>Faster parallel computing via the <code>future</code> package for <code><a href="../reference/as.sir.html">as.sir()</a></code> and <code><a href="../reference/antibiogram.html">wisca()</a></code>: a non-sequential plan (e.g. <code>future::plan(future::multisession)</code>) must be active before using <code>parallel = TRUE</code>.</li>
</ul></div> </ul></div>
<div class="section level4"> <div class="section level4">
<h4 id="new-3-0-1-9081">New<a class="anchor" aria-label="anchor" href="#new-3-0-1-9081"></a></h4> <h4 id="new-3-0-1-9082">New<a class="anchor" aria-label="anchor" href="#new-3-0-1-9082"></a></h4>
<ul><li>EUCAST 2026 and CLSI 2026 breakpoints: over 5,700 new breakpoints added to the <code>clinical_breakpoints</code> data set; EUCAST 2026 is now the default for all MIC and disk diffusion interpretations</li> <ul><li>EUCAST 2026 and CLSI 2026 breakpoints: over 5,700 new breakpoints added to the <code>clinical_breakpoints</code> data set; EUCAST 2026 is now the default for all MIC and disk diffusion interpretations</li>
<li>Wildtype/Non-wildtype (WT/NWT) output when using ECOFF-based interpretation, by setting <code>breakpoint_type = "ECOFF"</code> in <code><a href="../reference/as.sir.html">as.sir()</a></code>; WT/NWT results are fully supported in all resistance/susceptibility functions and plots (<a href="https://github.com/msberends/AMR/issues/254" class="external-link">#254</a>)</li> <li>Wildtype/Non-wildtype (WT/NWT) output when using ECOFF-based interpretation, by setting <code>breakpoint_type = "ECOFF"</code> in <code><a href="../reference/as.sir.html">as.sir()</a></code>; WT/NWT results are fully supported in all resistance/susceptibility functions and plots (<a href="https://github.com/msberends/AMR/issues/254" class="external-link">#254</a>)</li>
<li> <li>
@@ -74,7 +74,7 @@
<li>New <code><a href="../reference/antibiogram.html">wisca_plot()</a></code> to assess the susceptibility and incidence distributions from the Monte Carlo simulations</li> <li>New <code><a href="../reference/antibiogram.html">wisca_plot()</a></code> to assess the susceptibility and incidence distributions from the Monte Carlo simulations</li>
</ul></div> </ul></div>
<div class="section level4"> <div class="section level4">
<h4 id="fixed-3-0-1-9081">Fixed<a class="anchor" aria-label="anchor" href="#fixed-3-0-1-9081"></a></h4> <h4 id="fixed-3-0-1-9082">Fixed<a class="anchor" aria-label="anchor" href="#fixed-3-0-1-9082"></a></h4>
<ul><li>Setting <code>options(AMR_guideline = "EUCAST 2012")</code> or any year-qualified value no longer causes errors or silent wrong behaviour in <code><a href="../reference/interpretive_rules.html">interpretive_rules()</a></code>, <code><a href="../reference/proportion.html">resistance()</a></code>, <code><a href="../reference/proportion.html">susceptibility()</a></code>, <code><a href="../reference/count.html">count_resistant()</a></code>, <code><a href="../reference/count.html">count_susceptible()</a></code>, and SIR plotting/printing functions (<a href="https://github.com/msberends/AMR/issues/298" class="external-link">#298</a>)</li> <ul><li>Setting <code>options(AMR_guideline = "EUCAST 2012")</code> or any year-qualified value no longer causes errors or silent wrong behaviour in <code><a href="../reference/interpretive_rules.html">interpretive_rules()</a></code>, <code><a href="../reference/proportion.html">resistance()</a></code>, <code><a href="../reference/proportion.html">susceptibility()</a></code>, <code><a href="../reference/count.html">count_resistant()</a></code>, <code><a href="../reference/count.html">count_susceptible()</a></code>, and SIR plotting/printing functions (<a href="https://github.com/msberends/AMR/issues/298" class="external-link">#298</a>)</li>
<li> <li>
<code><a href="../reference/as.sir.html">as.sir()</a></code> <code><a href="../reference/as.sir.html">as.sir()</a></code>
@@ -103,7 +103,7 @@
</li> </li>
</ul></div> </ul></div>
<div class="section level4"> <div class="section level4">
<h4 id="updated-3-0-1-9081">Updated<a class="anchor" aria-label="anchor" href="#updated-3-0-1-9081"></a></h4> <h4 id="updated-3-0-1-9082">Updated<a class="anchor" aria-label="anchor" href="#updated-3-0-1-9082"></a></h4>
<ul><li> <ul><li>
<code><a href="../reference/top_n_microorganisms.html">top_n_microorganisms()</a></code>: new <code>property_for_each</code> argument for sub-grouping within top <em>n</em> groups; rank ordering enforced (only lower taxonomic ranks allowed); fixed <code>property = NULL</code> not being accepted; inner filter now tracks original row indices to prevent cross-group contamination</li> <code><a href="../reference/top_n_microorganisms.html">top_n_microorganisms()</a></code>: new <code>property_for_each</code> argument for sub-grouping within top <em>n</em> groups; rank ordering enforced (only lower taxonomic ranks allowed); fixed <code>property = NULL</code> not being accepted; inner filter now tracks original row indices to prevent cross-group contamination</li>
<li>Taxonomic update for all microorganisms, now updated to June 2026</li> <li>Taxonomic update for all microorganisms, now updated to June 2026</li>

2
news/index.md
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@@ -1,6 +1,6 @@
# Changelog # Changelog
## AMR 3.0.1.9081 ## AMR 3.0.1.9082
Planned as v3.1.0, end of June 2026. Planned as v3.1.0, end of June 2026.

2
pkgdown.yml
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@@ -10,7 +10,7 @@ articles:
PCA: PCA.html PCA: PCA.html
WHONET: WHONET.html WHONET: WHONET.html
WISCA: WISCA.html WISCA: WISCA.html
last_built: 2026-06-27T13:36Z last_built: 2026-07-03T17:18Z
urls: urls:
reference: https://amr-for-r.org/reference reference: https://amr-for-r.org/reference
article: https://amr-for-r.org/articles article: https://amr-for-r.org/articles

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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9081</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9082</small>
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2
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@@ -9,7 +9,7 @@ options(AMR_guideline = "CLSI")'><meta property="og:image" content="https://amr-
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9081</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9082</small>
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2
reference/AMR.html
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@@ -21,7 +21,7 @@ The AMR package is available in English, Arabic, Bengali, Chinese, Czech, Danish
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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2
reference/WHOCC.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9081</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9082</small>
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2
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9081</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9082</small>
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2
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9081</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9082</small>
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2
reference/add_custom_antimicrobials.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9081</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9082</small>
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2
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9081</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9082</small>
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22
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9081</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9082</small>
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@@ -112,16 +112,16 @@
<span class="r-in"><span></span></span> <span class="r-in"><span></span></span>
<span class="r-in"><span><span class="va">df</span></span></span> <span class="r-in"><span><span class="va">df</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> birth_date age age_exact age_at_y2k</span> <span class="r-out co"><span class="r-pr">#&gt;</span> birth_date age age_exact age_at_y2k</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 1999-06-30 26 26.99178 0</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 1 1999-06-30 27 27.00822 0</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 1968-01-29 58 58.40822 31</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 2 1968-01-29 58 58.42466 31</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 1965-12-05 60 60.55890 34</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 3 1965-12-05 60 60.57534 34</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 1980-03-01 46 46.32329 19</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 4 1980-03-01 46 46.33973 19</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 1949-11-01 76 76.65205 50</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 5 1949-11-01 76 76.66849 50</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 1947-02-14 79 79.36438 52</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 6 1947-02-14 79 79.38082 52</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 1940-02-19 86 86.35068 59</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 7 1940-02-19 86 86.36712 59</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 1988-01-10 38 38.46027 11</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 8 1988-01-10 38 38.47671 11</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 1997-08-27 28 28.83288 2</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 9 1997-08-27 28 28.84932 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 1978-01-26 48 48.41644 21</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 10 1978-01-26 48 48.43288 21</span>
</code></pre></div> </code></pre></div>
</div> </div>
</main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2> </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>

20
reference/age.md
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@@ -81,14 +81,14 @@ df$age_at_y2k <- age(df$birth_date, "2000-01-01")
df df
#> birth_date age age_exact age_at_y2k #> birth_date age age_exact age_at_y2k
#> 1 1999-06-30 26 26.99178 0 #> 1 1999-06-30 27 27.00822 0
#> 2 1968-01-29 58 58.40822 31 #> 2 1968-01-29 58 58.42466 31
#> 3 1965-12-05 60 60.55890 34 #> 3 1965-12-05 60 60.57534 34
#> 4 1980-03-01 46 46.32329 19 #> 4 1980-03-01 46 46.33973 19
#> 5 1949-11-01 76 76.65205 50 #> 5 1949-11-01 76 76.66849 50
#> 6 1947-02-14 79 79.36438 52 #> 6 1947-02-14 79 79.38082 52
#> 7 1940-02-19 86 86.35068 59 #> 7 1940-02-19 86 86.36712 59
#> 8 1988-01-10 38 38.46027 11 #> 8 1988-01-10 38 38.47671 11
#> 9 1997-08-27 28 28.83288 2 #> 9 1997-08-27 28 28.84932 2
#> 10 1978-01-26 48 48.41644 21 #> 10 1978-01-26 48 48.43288 21
``` ```

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@@ -7,7 +7,7 @@
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@@ -7,7 +7,7 @@
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2
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@@ -7,7 +7,7 @@
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@@ -13,7 +13,7 @@ All antibiogram types adhere to previously described approaches (see Source), an
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@@ -17,7 +17,7 @@ my_data_with_all_these_columns %&amp;gt;%
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2
reference/antimicrobials.html
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@@ -9,7 +9,7 @@ The antibiotics data set has been renamed to antimicrobials. The old name will b
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2
reference/as.ab.html
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@@ -7,7 +7,7 @@
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reference/as.av.html
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@@ -7,7 +7,7 @@
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reference/as.disk.html
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@@ -7,7 +7,7 @@
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2
reference/as.mic.html
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@@ -7,7 +7,7 @@
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2
reference/as.mo.html
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@@ -7,7 +7,7 @@
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10
reference/as.sir.html
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@@ -9,7 +9,7 @@ Breakpoints are currently implemented from EUCAST 2011-2026 and CLSI 2011-2026,
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@@ -462,10 +462,10 @@ Breakpoints are currently implemented from EUCAST 2011-2026 and CLSI 2011-2026,
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 4 × 18</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 4 × 18</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> datetime index method ab_given mo_given host_given input_given</span> <span class="r-out co"><span class="r-pr">#&gt;</span> datetime index method ab_given mo_given host_given input_given</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dttm&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dttm&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> 2026-06-27 <span style="color: #949494;">13:38:17</span> 1 MIC amoxicillin Escherich… human 8 </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> 2026-07-03 <span style="color: #949494;">17:20:53</span> 1 MIC amoxicillin Escherich… human 8 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> 2026-06-27 <span style="color: #949494;">13:38:17</span> 1 MIC cipro Escherich… human 0.256 </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> 2026-07-03 <span style="color: #949494;">17:20:53</span> 1 MIC cipro Escherich… human 0.256 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> 2026-06-27 <span style="color: #949494;">13:38:17</span> 1 DISK tobra Escherich… human 16 </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> 2026-07-03 <span style="color: #949494;">17:20:53</span> 1 DISK tobra Escherich… human 16 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">4</span> 2026-06-27 <span style="color: #949494;">13:38:18</span> 1 DISK genta Escherich… human 18 </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">4</span> 2026-07-03 <span style="color: #949494;">17:20:53</span> 1 DISK genta Escherich… human 18 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 11 more variables: ab &lt;ab&gt;, mo &lt;mo&gt;, host &lt;chr&gt;, input &lt;chr&gt;,</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 11 more variables: ab &lt;ab&gt;, mo &lt;mo&gt;, host &lt;chr&gt;, input &lt;chr&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># outcome &lt;sir&gt;, notes &lt;chr&gt;, guideline &lt;chr&gt;, ref_table &lt;chr&gt;, uti &lt;lgl&gt;,</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># outcome &lt;sir&gt;, notes &lt;chr&gt;, guideline &lt;chr&gt;, ref_table &lt;chr&gt;, uti &lt;lgl&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># breakpoint_S_R &lt;chr&gt;, site &lt;chr&gt;</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># breakpoint_S_R &lt;chr&gt;, site &lt;chr&gt;</span></span>

8
reference/as.sir.md
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@@ -712,10 +712,10 @@ sir_interpretation_history()
#> # A tibble: 4 × 18 #> # A tibble: 4 × 18
#> datetime index method ab_given mo_given host_given input_given #> datetime index method ab_given mo_given host_given input_given
#> <dttm> <int> <chr> <chr> <chr> <chr> <chr> #> <dttm> <int> <chr> <chr> <chr> <chr> <chr>
#> 1 2026-06-27 13:38:17 1 MIC amoxicillin Escherich… human 8 #> 1 2026-07-03 17:20:53 1 MIC amoxicillin Escherich… human 8
#> 2 2026-06-27 13:38:17 1 MIC cipro Escherich… human 0.256 #> 2 2026-07-03 17:20:53 1 MIC cipro Escherich… human 0.256
#> 3 2026-06-27 13:38:17 1 DISK tobra Escherich… human 16 #> 3 2026-07-03 17:20:53 1 DISK tobra Escherich… human 16
#> 4 2026-06-27 13:38:18 1 DISK genta Escherich… human 18 #> 4 2026-07-03 17:20:53 1 DISK genta Escherich… human 18
#> # ℹ 11 more variables: ab <ab>, mo <mo>, host <chr>, input <chr>, #> # ℹ 11 more variables: ab <ab>, mo <mo>, host <chr>, input <chr>,
#> # outcome <sir>, notes <chr>, guideline <chr>, ref_table <chr>, uti <lgl>, #> # outcome <sir>, notes <chr>, guideline <chr>, ref_table <chr>, uti <lgl>,
#> # breakpoint_S_R <chr>, site <chr> #> # breakpoint_S_R <chr>, site <chr>

2
reference/atc_online.html
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@@ -7,7 +7,7 @@
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reference/av_from_text.html
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@@ -7,7 +7,7 @@
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reference/av_property.html
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@@ -7,7 +7,7 @@
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reference/availability.html
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@@ -7,7 +7,7 @@
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reference/bug_drug_combinations.html
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@@ -7,7 +7,7 @@
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reference/clinical_breakpoints.html
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@@ -21,7 +21,7 @@ Use as.sir() to transform MICs or disks measurements to SIR values."><meta prope
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reference/count.html
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@@ -9,7 +9,7 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
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reference/custom_interpretive_rules.html
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@@ -7,7 +7,7 @@
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reference/custom_mdro_guideline.html
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@@ -7,7 +7,7 @@
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reference/dosage.html
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@@ -7,7 +7,7 @@
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reference/esbl_isolates.html
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@@ -7,7 +7,7 @@
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reference/example_isolates.html
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@@ -7,7 +7,7 @@
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reference/example_isolates_unclean.html
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@@ -7,7 +7,7 @@
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reference/export_ncbi_biosample.html
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@@ -7,7 +7,7 @@
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reference/first_isolate.html
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@@ -9,7 +9,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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reference/g.test.html
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@@ -7,7 +7,7 @@
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reference/get_episode.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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reference/ggplot_pca.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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reference/ggplot_sir.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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reference/guess_ab_col.html
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@@ -7,7 +7,7 @@
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reference/index.html
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@@ -7,7 +7,7 @@
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reference/interpretive_rules.html
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@@ -9,7 +9,7 @@ To improve the interpretation of the antibiogram before CLSI/EUCAST interpretive
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reference/intrinsic_resistant.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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reference/italicise_taxonomy.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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reference/join.html
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@@ -7,7 +7,7 @@
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2
reference/key_antimicrobials.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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reference/kurtosis.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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reference/like.html
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@@ -7,7 +7,7 @@
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reference/mdro.html
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@@ -7,7 +7,7 @@
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2
reference/mean_amr_distance.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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reference/microorganisms.codes.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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2
reference/microorganisms.groups.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9081</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9082</small>
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2
reference/microorganisms.html
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@@ -9,7 +9,7 @@ This data set is carefully crafted, yet made 100% reproducible from public and a
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9081</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9082</small>
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2
reference/mo_matching_score.html
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@@ -7,7 +7,7 @@
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2
reference/mo_property.html
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@@ -7,7 +7,7 @@
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9081</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9082</small>
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2
reference/mo_source.html
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@@ -9,7 +9,7 @@ This is the fastest way to have your organisation (or analysis) specific codes p
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2
reference/pca.html
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@@ -7,7 +7,7 @@
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9081</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9082</small>
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2
reference/plot.html
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@@ -9,7 +9,7 @@ Especially the scale_*_mic() functions are relevant wrappers to plot MIC values
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9081</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9082</small>
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2
reference/proportion.html
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@@ -9,7 +9,7 @@ resistance() should be used to calculate resistance, susceptibility() should be
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9081</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9082</small>
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2
reference/random.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9081</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9082</small>
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2
reference/resistance_predict.html
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@@ -9,7 +9,7 @@ NOTE: These functions are deprecated and will be removed in a future version. Us
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9081</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9082</small>
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2
reference/skewness.html
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@@ -9,7 +9,7 @@ When negative ('left-skewed'): the left tail is longer; the mass of the distribu
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9081</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9082</small>
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2
reference/top_n_microorganisms.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9081</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9082</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

2
reference/translate.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9081</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9082</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

2
search.json
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